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AB update
This commit is contained in:
Kevin Gasperich
Kevin Gasperich
parent
1daa85ffb9
commit
e9842cae9b
@ -214,22 +214,59 @@ def convert_kpts(filename,qph5path):
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# #
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##########################################
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#with h5py.File(qph5path,'r') as qph5:
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# ezfio.set_ao_basis_ao_basis(qph5['ao_basis'].attrs['ao_basis'])
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# ezfio.set_ao_basis_ao_nucl(qph5['ao_basis/ao_nucl'][()].tolist())
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#
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#
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#Just need one (can clean this up later)
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# ao_prim_num_max = 5
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#
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# d = [ [0] *ao_prim_num_max]*ao_num
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# ezfio.set_ao_basis_ao_prim_num([ao_prim_num_max]*ao_num)
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# ezfio.set_ao_basis_ao_power(d)
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# ezfio.set_ao_basis_ao_coef(d)
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# ezfio.set_ao_basis_ao_expo(d)
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##########################################
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# #
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# Basis #
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# #
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##########################################
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with h5py.File(qph5path,'r') as qph5:
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do_pseudo = qph5['pseudo'].attrs['do_pseudo']
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ezfio.set_pseudo_do_pseudo(do_pseudo)
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if (do_pseudo):
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ezfio.set_pseudo_pseudo_lmax(qph5['pseudo'].attrs['pseudo_lmax'])
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ezfio.set_pseudo_pseudo_klocmax(qph5['pseudo'].attrs['pseudo_klocmax'])
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ezfio.set_pseudo_pseudo_kmax(qph5['pseudo'].attrs['pseudo_kmax'])
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ezfio.set_pseudo_nucl_charge_remove(qph5['pseudo/nucl_charge_remove'][()].tolist())
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ezfio.set_pseudo_pseudo_n_k(qph5['pseudo/pseudo_n_k'][()].tolist())
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ezfio.set_pseudo_pseudo_n_kl(qph5['pseudo/pseudo_n_kl'][()].tolist())
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ezfio.set_pseudo_pseudo_v_k(qph5['pseudo/pseudo_v_k'][()].tolist())
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ezfio.set_pseudo_pseudo_v_kl(qph5['pseudo/pseudo_v_kl'][()].tolist())
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ezfio.set_pseudo_pseudo_dz_k(qph5['pseudo/pseudo_dz_k'][()].tolist())
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ezfio.set_pseudo_pseudo_dz_kl(qph5['pseudo/pseudo_dz_kl'][()].tolist())
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##########################################
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# #
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# Basis #
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# #
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##########################################
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with h5py.File(qph5path,'r') as qph5:
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coeftmp = qph5['ao_basis/ao_coef'][()]
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expotmp = qph5['ao_basis/ao_expo'][()]
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ezfio.set_ao_basis_ao_basis(qph5['ao_basis'].attrs['ao_basis'])
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ezfio.set_ao_basis_ao_nucl(qph5['ao_basis/ao_nucl'][()].tolist())
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#Just need one (can clean this up later)
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ao_prim_num_max = 5
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d = [ [0] *ao_prim_num_max]*ao_num
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ezfio.set_ao_basis_ao_prim_num([ao_prim_num_max]*ao_num)
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ezfio.set_ao_basis_ao_power(d)
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ezfio.set_ao_basis_ao_coef(d)
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ezfio.set_ao_basis_ao_expo(d)
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ezfio.set_ao_basis_ao_prim_num(qph5['ao_basis/ao_prim_num'][()].tolist())
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ezfio.set_ao_basis_ao_power(qph5['ao_basis/ao_power'][()].tolist())
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ezfio.set_ao_basis_ao_coef(qph5['ao_basis/ao_coef'][()].tolist())
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ezfio.set_ao_basis_ao_expo(qph5['ao_basis/ao_expo'][()].tolist())
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##########################################
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# #
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@ -404,20 +441,57 @@ def convert_cplx(filename,qph5path):
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# #
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##########################################
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# with h5py.File(qph5path,'r') as qph5:
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# ezfio.set_ao_basis_ao_basis(qph5['ao_basis'].attrs['ao_basis'])
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# ezfio.set_ao_basis_ao_nucl(qph5['ao_basis/ao_nucl'][()].tolist())
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#
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#
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# #Just need one (can clean this up later)
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# ao_prim_num_max = 5
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#
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# d = [ [0] *ao_prim_num_max]*ao_num
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# ezfio.set_ao_basis_ao_prim_num([ao_prim_num_max]*ao_num)
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# ezfio.set_ao_basis_ao_power(d)
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# ezfio.set_ao_basis_ao_coef(d)
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# ezfio.set_ao_basis_ao_expo(d)
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##########################################
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# #
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# Basis #
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# #
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##########################################
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with h5py.File(qph5path,'r') as qph5:
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do_pseudo = qph5['pseudo'].attrs['do_pseudo']
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ezfio.set_pseudo_do_pseudo(do_pseudo)
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if (do_pseudo):
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ezfio.set_pseudo_pseudo_lmax(qph5['pseudo'].attrs['pseudo_lmax'])
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ezfio.set_pseudo_pseudo_klocmax(qph5['pseudo'].attrs['pseudo_klocmax'])
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ezfio.set_pseudo_pseudo_kmax(qph5['pseudo'].attrs['pseudo_kmax'])
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ezfio.set_pseudo_nucl_charge_remove(qph5['pseudo/nucl_charge_remove'][()].tolist())
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ezfio.set_pseudo_pseudo_n_k(qph5['pseudo/pseudo_n_k'][()].tolist())
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ezfio.set_pseudo_pseudo_n_kl(qph5['pseudo/pseudo_n_kl'][()].tolist())
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ezfio.set_pseudo_pseudo_v_k(qph5['pseudo/pseudo_v_k'][()].tolist())
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ezfio.set_pseudo_pseudo_v_kl(qph5['pseudo/pseudo_v_kl'][()].tolist())
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ezfio.set_pseudo_pseudo_dz_k(qph5['pseudo/pseudo_dz_k'][()].tolist())
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ezfio.set_pseudo_pseudo_dz_kl(qph5['pseudo/pseudo_dz_kl'][()].tolist())
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##########################################
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# #
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# Basis #
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# #
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##########################################
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with h5py.File(qph5path,'r') as qph5:
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coeftmp = qph5['ao_basis/ao_coef'][()]
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expotmp = qph5['ao_basis/ao_expo'][()]
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ezfio.set_ao_basis_ao_basis(qph5['ao_basis'].attrs['ao_basis'])
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ezfio.set_ao_basis_ao_nucl(qph5['ao_basis/ao_nucl'][()].tolist())
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#Just need one (can clean this up later)
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ao_prim_num_max = 5
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d = [ [0] *ao_prim_num_max]*ao_num
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ezfio.set_ao_basis_ao_prim_num([ao_prim_num_max]*ao_num)
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ezfio.set_ao_basis_ao_power(d)
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ezfio.set_ao_basis_ao_coef(d)
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ezfio.set_ao_basis_ao_expo(d)
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ezfio.set_ao_basis_ao_prim_num(qph5['ao_basis/ao_prim_num'][()].tolist())
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ezfio.set_ao_basis_ao_power(qph5['ao_basis/ao_power'][()].tolist())
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ezfio.set_ao_basis_ao_coef(qph5['ao_basis/ao_coef'][()].tolist())
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ezfio.set_ao_basis_ao_expo(qph5['ao_basis/ao_expo'][()].tolist())
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@ -603,6 +603,8 @@ def pyscf2QP2(cell,mf, kpts, kmesh=None, cas_idx=None, int_threshold = 1E-8,
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qph5.create_group('electrons')
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qph5.create_group('ao_basis')
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qph5.create_group('mo_basis')
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qph5.create_group('pseudo')
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qph5['pseudo'].attrs['do_pseudo']=False
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qph5.create_group('PBC_DATA')
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mo_coeff = mf.mo_coeff
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@ -671,19 +673,13 @@ def pyscf2QP2(cell,mf, kpts, kmesh=None, cas_idx=None, int_threshold = 1E-8,
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# shell start,end; AO start,end (sph or cart) for each atom
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for ib in range(sh0,sh1): # sets of contracted exponents
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l = cell.bas_angular(ib) # angular momentum
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if ( cell.cart==True):
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representation=((l+1)*(l+2))//2
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else:
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representation=2*l-1
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nprim = cell.bas_nprim(ib) # numer of primitives
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es = cell.bas_exp(ib) # exponents
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cs = cell.bas_ctr_coeff(ib) # coeffs
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nctr = cell.bas_nctr(ib) # number of contractions
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print(iatom,ib,l,nprim,nctr,tmp_idx)
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for ic in range(nctr): # sets of contraction coeffs
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# for nfunc in range(((l+1)*(l+2))//2): # always use cart for qp ao basis?
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# for nfunc in range(2*l-1):
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for nfunc in range(representation):
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for nfunc in range(((l+1)*(l+2))//2): # always use cart for qp ao basis?
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qp_expo[tmp_idx,:nprim] = es[:]
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qp_coef[tmp_idx,:nprim] = cs[:,ic]
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qp_nucl[tmp_idx] = iatom + 1
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@ -876,8 +872,83 @@ def pyscf2QP2(cell,mf, kpts, kmesh=None, cas_idx=None, int_threshold = 1E-8,
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qph5.create_dataset('PBC_DATA/Super_Twist',(1,3),dtype="f8",data=sp_twist)
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qph5.create_dataset('PBC_DATA/LatticeVectors',(3,3),dtype="f8",data=cell.lattice_vectors())
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qph5.create_dataset('PBC_DATA/eigenval',(1,nmo),dtype="f8",data=mf.mo_energy)
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##########################################
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# #
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# ECP #
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# #
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##########################################
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if (cell.has_ecp()):
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#atsymb = [mol.atom_pure_symbol(i) for i in range(natom)]
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#pyecp = mol._ecp
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## nelec to remove for each atom
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#nuc_z_remov = [pyecp[i][0] for i in atsymb]
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#nl_per_atom = [len(pyecp[i][1]) for i in atsymb]
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## list of l-values for channels of each atom
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#ecp_l = [[pyecp[i][1][j][0] for j in range(len(pyecp[i][1]))] for i in atsymb]
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## list of [exp,coef] for each channel (r**0,1,2,3,4,5,)
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#ecp_ac = [[pyecp[i][1][j][1] for j in range(len(pyecp[i][1]))] for i in atsymb]
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pyecp = [cell._ecp[cell.atom_pure_symbol(i)] for i in range(natom)]
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nzrmv=[0]*natom
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lmax=0
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klocmax=0
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knlmax=0
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for i,(nz,dat) in enumerate(pyecp):
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nzrmv[i]=nz
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for lval,ac in dat:
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if (lval==-1):
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klocmax=max(sum(len(j) for j in ac),klocmax)
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else:
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lmax=max(lval,lmax)
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knlmax=max(sum(len(j) for j in ac),knlmax)
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#psd_nk = np.zeros((natom,klocmax),dtype=int)
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#psd_vk = np.zeros((natom,klocmax),dtype=float)
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#psd_dzk = np.zeros((natom,klocmax),dtype=float)
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#psd_nkl = np.zeros((natom,knlmax,lmax+1),dtype=int)
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#psd_vkl = np.zeros((natom,knlmax,lmax+1),dtype=float)
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#psd_dzkl = np.zeros((natom,knlmax,lmax+1),dtype=float)
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klnlmax=max(klocmax,knlmax)
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psd_n = np.zeros((lmax+2,klnlmax,natom),dtype=int)
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psd_v = np.zeros((lmax+2,klnlmax,natom),dtype=float)
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psd_dz = np.zeros((lmax+2,klnlmax,natom),dtype=float)
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for i,(_,dat) in enumerate(pyecp):
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for lval,ac in dat:
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count=0
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for ri,aici in enumerate(ac):
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for ai,ci in aici:
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psd_n[lval+1,count,i] = ri-2
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psd_v[lval+1,count,i] = ci
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psd_dz[lval+1,count,i] = ai
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count += 1
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psd_nk = psd_n[0,:klocmax]
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psd_vk = psd_v[0,:klocmax]
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psd_dzk = psd_dz[0,:klocmax]
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psd_nkl = psd_n[1:,:knlmax]
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psd_vkl = psd_v[1:,:knlmax]
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psd_dzkl = psd_dz[1:,:knlmax]
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with h5py.File(qph5path,'a') as qph5:
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qph5['pseudo'].attrs['do_pseudo']=True
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qph5['pseudo'].attrs['pseudo_lmax']=lmax
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qph5['pseudo'].attrs['pseudo_klocmax']=klocmax
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qph5['pseudo'].attrs['pseudo_kmax']=knlmax
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qph5.create_dataset('pseudo/nucl_charge_remove',data=nzrmv)
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qph5.create_dataset('pseudo/pseudo_n_k',data=psd_nk)
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qph5.create_dataset('pseudo/pseudo_n_kl',data=psd_nkl)
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qph5.create_dataset('pseudo/pseudo_v_k',data=psd_vk)
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qph5.create_dataset('pseudo/pseudo_v_kl',data=psd_vkl)
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qph5.create_dataset('pseudo/pseudo_dz_k',data=psd_dzk)
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qph5.create_dataset('pseudo/pseudo_dz_kl',data=psd_dzkl)
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## nelec to remove for each atom
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#nuc_z_remov = [i[0] for i in pyecp]
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#nl_per_atom = [len(i[1]) for i in pyecp]
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## list of l-values for channels of each atom
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#ecp_l = [[ j[0] for j in i[1] ] for i in pyecp]
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#lmax = max(map(max,ecp_l))
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## list of [exp,coef] for each channel (r**0,1,2,3,4,5,)
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#ecp_ac = [[ j[1] for j in i[1] ] for i in pyecp]
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return
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